| Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors L Zapata, G Caravagna, MJ Williams, E Lakatos, K AbdulJabbar, ... Nature Genetics 55 (3), 451-460, 2023 | 47 | 2023 |
| Negative selection may cause grossly altered but broadly stable karyotypes in metastatic colorectal cancer W Cross, S Nowinski, GD Cresswell, M Mossner, A Banerjee, B Lu, ... Biorxiv, 2020.03. 26.007138, 2020 | 20 | 2020 |
| Clonal KEAP1 mutations with loss of heterozygosity share reduced immunotherapy efficacy and low immune cell infiltration in lung adenocarcinoma S Scalera, B Ricciuti, M Mazzotta, N Calonaci, JV Alessi, L Cipriani, G Bon, ... Annals of Oncology 34 (3), 275-288, 2023 | 17 | 2023 |
| Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc A Antonello, R Bergamin, N Calonaci, J Househam, S Milite, MJ Williams, ... Genome Biology 25 (1), 38, 2024 | 14* | 2024 |
| A Bayesian method to cluster single-cell RNA sequencing data using copy number alterations S Milite, R Bergamin, L Patruno, N Calonaci, G Caravagna Bioinformatics 38 (9), 2512-2518, 2022 | 12 | 2022 |
| Transcriptional characterization of stage I epithelial ovarian cancer: a multicentric study E Calura, M Ciciani, A Sambugaro, L Paracchini, G Benvenuto, S Milite, ... Cells 8 (12), 1554, 2019 | 12 | 2019 |
| Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer H Kayhanian, W Cross, SEM van der Horst, P Barmpoutis, E Lakatos, ... Nature Genetics 56 (7), 1420-1433, 2024 | 9* | 2024 |
| Epigenetic heritability of cell plasticity drives cancer drug resistance through one-to-many genotype to phenotype mapping J Fernandez-Mateos, S Milite, E Oliveira, G Vlachogiannis, B Chen, ... bioRxiv, 2023.11. 15.567140, 2023 | 3 | 2023 |
| A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing L Patruno, S Milite, R Bergamin, N Calonaci, A D’Onofrio, F Anselmi, ... PLOS Computational Biology 19 (11), e1011557, 2023 | 3 | 2023 |
| Deep Archetypal Analysis for interpretable multi-omic data integration based on biological principles S Milite, G Caravagna, A Sottoriva bioRxiv, 2024.04. 05.588238, 2024 | 1 | 2024 |
| Clinical application of tumour-in-normal contamination assessment from whole genome sequencing J Mitchell, S Milite, J Bartram, S Walker, N Volkova, O Yavorska, ... Nature Communications 15 (1), 323, 2024 | 1 | 2024 |
| NeuroVelo: interpretable learning of cellular dynamics from single-cell transcriptomic data I Kouadri Boudjelthia, S Milite, N El Kazwini, J Fernandez-Mateos, ... bioRxiv, 2023.11. 17.567500, 2023 | 1 | 2023 |
| 180P Unravelling drug resistance in high-grade serous ovarian cancer through clonal dynamics and single-cell heterogeneity analysis AHIR Garces, F Whiting, S Milite, E Oliveira, L Pickard, S Banerjee, ... ESMO Open 9, 2024 | | 2024 |
| NeuroVelo: interpretable learning of temporal cellular dynamics from single-cell data IK Boudjelthia, S Milite, N El Kazwini, Y Huang, A Sottoriva, G Sanguinetti | | 2024 |
| Timing copy number alterations in Barrett's oesophagus in absolute time C Gabbutt, W Cross, S Milite, G Caravagna, A Sottoriva, TG Paulson, ... JOURNAL OF PATHOLOGY 264, S4-S4, 2024 | | 2024 |
| Mutation frequency and copy number alterations determine prognosis and metastatic tropism in 60,000 clinical cancer samples N Calonaci, E Krasniqi, S Scalera, G Gandolfi, S Milite, B Ricciuti, ... medRxiv, 2024.05. 13.24307238, 2024 | | 2024 |
| A Bayesian framework to infer and cluster mutational signatures leveraging prior biological knowledge. E Buscaroli, AS Haghighi, R Bergamin, S Milite, ENV Garcia, A Tasciotti, ... bioRxiv, 2024.09. 16.613266, 2024 | | 2024 |
| NeuroVelo: interpretable learning of cellular dynamics from single-cell transcriptomic data IK Boudjelthia, S Milite, N El Kazwini, J Fernandez-Mateos, N Valeri, ... | | 2023 |
| Time of Origin and Environmental Drivers of Leukemia Immune Escape after Transplantation C Toffalori, R Bergamin, A Antonello, AF Tortorelli, G Orofino, M Cristante, ... Blood 142, 362, 2023 | | 2023 |
| Clonal Evolution of Chronic Lymphocytic Leukemia with Bimodal CD49d Expression Reveals CD49d Plasticity E Tissino, N Calonaci, F Pozzo, G Forestieri, L Terzi Di Bergamo, F Vit, ... Blood 140 (Supplement 1), 9844-9846, 2022 | | 2022 |
